Magnesium in PDB 6om4: The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca

Protein crystallography data

The structure of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca, PDB code: 6om4 was solved by S.-H.Dong, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.98 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.094, 76.059, 131.902, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 19.9

Other elements in 6om4:

The structure of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca (pdb code 6om4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca, PDB code: 6om4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6om4

Go back to Magnesium Binding Sites List in 6om4
Magnesium binding site 1 out of 4 in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:17.2
occ:1.00
O A:HOH518 2.1 17.7 1.0
O A:HOH516 2.1 22.7 1.0
O A:HOH591 2.1 17.9 1.0
O6 A:POP403 2.1 15.6 1.0
OD2 A:ASP148 2.1 18.6 1.0
O A:HOH585 2.2 18.4 1.0
CG A:ASP148 3.1 18.8 1.0
P2 A:POP403 3.3 16.6 1.0
OD1 A:ASP148 3.5 17.4 1.0
O5 A:POP403 3.6 16.5 1.0
NZ A:LYS170 4.0 16.5 1.0
OE1 A:GLU151 4.1 27.8 1.0
O A:GLN149 4.1 20.1 1.0
CD A:GLU151 4.1 27.4 1.0
O3 A:POP403 4.2 18.8 1.0
O A:POP403 4.2 17.2 1.0
OE2 A:GLU151 4.2 29.4 1.0
OD1 A:ASN154 4.3 19.1 1.0
ND2 A:ASN154 4.3 12.1 1.0
O4 A:POP403 4.4 18.3 1.0
CB A:ASP148 4.4 18.7 1.0
CE A:LYS170 4.5 16.4 1.0
CG A:ASN154 4.8 15.4 1.0
CG A:GLU151 4.8 23.1 1.0
P1 A:POP403 4.9 17.9 1.0

Magnesium binding site 2 out of 4 in 6om4

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Magnesium binding site 2 out of 4 in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:17.3
occ:1.00
O2 A:POP403 2.0 18.3 1.0
O1A C:ND7101 2.0 18.8 1.0
O5 A:POP403 2.0 16.5 1.0
O A:HOH623 2.1 18.8 1.0
O A:HOH568 2.2 15.9 1.0
O A:HOH532 2.3 15.3 1.0
P2 A:POP403 3.2 16.6 1.0
P1 A:POP403 3.2 17.9 1.0
O A:POP403 3.4 17.2 1.0
PA C:ND7101 3.5 21.3 1.0
O4 A:POP403 3.8 18.3 1.0
O3 A:POP403 3.9 18.8 1.0
O A:HOH627 4.1 24.6 1.0
OD2 A:ASP214 4.1 21.4 1.0
O A:HOH521 4.1 19.4 1.0
O A:HOH530 4.1 26.4 1.0
O A:HOH585 4.2 18.4 1.0
N3A C:ND7101 4.3 19.7 1.0
O5' C:ND7101 4.3 19.5 1.0
OD1 A:ASP214 4.3 20.7 1.0
C5' C:ND7101 4.3 18.9 1.0
O1 A:POP403 4.4 17.9 1.0
O6 A:POP403 4.4 15.6 1.0
O2A C:ND7101 4.5 18.9 1.0
CG A:ASP214 4.6 21.2 1.0
C3' C:ND7101 4.8 18.2 1.0

Magnesium binding site 3 out of 4 in 6om4

Go back to Magnesium Binding Sites List in 6om4
Magnesium binding site 3 out of 4 in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:30.2
occ:1.00
O3 B:POP404 1.9 26.4 1.0
O B:HOH587 2.0 24.5 1.0
OD2 B:ASP148 2.1 27.9 1.0
O B:HOH504 2.1 30.6 1.0
O B:HOH589 2.2 27.2 1.0
CG B:ASP148 3.2 29.2 1.0
P1 B:POP404 3.3 26.1 1.0
O1 B:POP404 3.6 22.8 1.0
OE2 B:GLU151 3.7 50.0 1.0
CD B:GLU151 3.7 37.8 1.0
OD1 B:ASP148 3.7 29.0 1.0
OE1 B:GLU151 3.9 40.3 1.0
NZ B:LYS170 4.0 22.4 1.0
O B:GLN149 4.1 19.0 1.0
O B:POP404 4.1 24.8 1.0
OD1 B:ASN154 4.2 20.8 1.0
O4 B:POP404 4.2 23.1 1.0
O2 B:POP404 4.2 25.0 1.0
CE B:LYS170 4.3 18.5 1.0
ND2 B:ASN154 4.3 13.2 1.0
CG B:GLU151 4.3 29.5 1.0
CB B:ASP148 4.5 23.9 1.0
CG B:ASN154 4.7 17.6 1.0
P2 B:POP404 4.9 24.6 1.0
CB B:GLU151 4.9 23.9 1.0

Magnesium binding site 4 out of 4 in 6om4

Go back to Magnesium Binding Sites List in 6om4
Magnesium binding site 4 out of 4 in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:21.0
occ:1.00
O6 B:POP404 2.0 24.1 1.0
O1 B:POP404 2.0 22.8 1.0
O2A D:ND7101 2.1 20.7 1.0
O B:HOH526 2.1 20.3 1.0
O B:HOH576 2.1 23.0 1.0
O B:HOH545 2.1 17.0 1.0
P1 B:POP404 3.2 26.1 1.0
P2 B:POP404 3.3 24.6 1.0
PA D:ND7101 3.5 19.8 1.0
O B:POP404 3.5 24.8 1.0
OD2 B:ASP214 4.0 17.8 1.0
O2 B:POP404 4.0 25.0 1.0
O B:HOH517 4.0 24.2 1.0
O4 B:POP404 4.0 23.1 1.0
O B:HOH589 4.2 27.2 1.0
OD1 B:ASP214 4.2 17.2 1.0
N3A D:ND7101 4.2 18.0 1.0
C5' D:ND7101 4.4 19.5 1.0
O5' D:ND7101 4.4 17.7 1.0
O D:HOH208 4.4 28.5 1.0
O3 B:POP404 4.5 26.4 1.0
O5 B:POP404 4.5 25.6 1.0
O1A D:ND7101 4.5 20.5 1.0
CG B:ASP214 4.5 17.0 1.0
O B:HOH704 4.7 29.5 1.0
C3' D:ND7101 4.8 19.1 1.0

Reference:

S.H.Dong, A.Kulikovsky, I.Zukher, P.Estrada, S.Dubiley, K.Severinov, S.K.Nair. Biosynthesis of the Ripp Trojan Horse Nucleotide Antibiotic Microcin C Is Directed By Then-Formyl of the Peptide Precursor. Chem Sci V. 10 2391 2019.
ISSN: ISSN 2041-6520
PubMed: 30881667
DOI: 10.1039/C8SC03173H
Page generated: Mon Dec 14 23:43:52 2020

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